configuration cap on retrieved maps and pathways

enrichment/config.txt

-type	resource
-map	https://pdmap.uni.lu/minerva/api/
-pathway	WikiPathways_2019_Human
-pathway	Panther_2016
+type	resource	value
parameter	max_areas_per_map	5
parameter	max_areas_per_pathway_db	5
map	https://pdmap.uni.lu/minerva/api/	
map	https://progeria.uni.lu/minerva/api/	
pathway_db	WikiPathways_2019_Human	
pathway_db	Panther_2016	
\ No newline at end of file

enrichment/enrich_maps.R

@@ -64,11 +64,11 @@ for(map in config[config$type == "map","resource"]) {
   message(paste0("Going through individual models..."))
   for(i in 1:length(model_elements)) {
     me <- model_elements[[i]]
-    pVals <- c()
-    pnames <- unique(me[me$type == "Pathway","name"])
+    if(length(unique(me[me$type == "Pathway","name"])) == 0) { next }
+    path_pVals <- data.frame(pname = unique(me[me$type == "Pathway","name"]), pVal = 1)
     ### Calculating the inclusion of the elements per bioentity set
-    for(up in pnames) {
-      res <- apply(me[me$name == up,"bounds"], 1, 
+    for(up in 1:nrow(path_pVals)) {
+      res <- apply(me[me$name == path_pVals$pname[up],"bounds"], 1, 
                    function(x) me$bounds$x >= x["x"] & me$bounds$x <= (x["x"] +  x["width"]) & 
                      me$bounds$y >= x["y"] & me$bounds$y <= (x["y"] +  x["height"]))
 
@@ -78,22 +78,28 @@ for(map in config[config$type == "map","resource"]) {
       k <- length(intersect(input,hgncs))
       
       if (k > 0) {
-        pVal <- (((m * (n - k)) / (k * (N - m))) ** k) * (((n * (N - m)) / (N * (n - k))) ** n)
-        pVals <- c(pVals, pVal)
-      } else {
-        pVals <- c(pVals, 1)
+        path_pVals$pVal[up] <- (((m * (n - k)) / (k * (N - m))) ** k) * (((n * (N - m)) / (N * (n - k))) ** n)
       }
     }
     ### Bonferroni correction
-    # pVals <- pVals*length(pVals)
-    if(length(pnames[pVals < 0.1])) {
-      pbounds <- cbind(name = me[me$name %in% pnames[pVals < 0.1],]$name,
-                       me[me$name %in% pnames[pVals < 0.1],]$bounds)
+    # path_pVals$pVal <- path_pVals$pVal*nrow(path_pVals)
+
+    path_pVals <- path_pVals[path_pVals$pVal < 0.1, ]
+
+    if(nrow(path_pVals) > 0) {
+      path_pVals <- path_pVals[order(path_pVals$pVal), ]
+      if(!is.null(config[config$resource == "max_areas_per_map",]$value)) {
+        path_pVals <- path_pVals[1:config[config$resource == "max_areas_per_map",]$value, ]
+      }
+      
+      pbounds <- cbind(name = me[me$name %in% path_pVals$pname,]$name,
+                       me[me$name %in% path_pVals$pname,]$bounds)
+      
       pathways_to_pull <- cbind(minerva_instance = map, 
                                 project_id = project_id, 
                                 model_id = models$idObject[i],
                                 pbounds, stringsAsFactors = F)
-    
+      
       write.table(pathways_to_pull, file = "enriched_disease_maps.txt",
                   sep = "\t", quote = F, col.names = F, row.names = F, append = T)
       message(paste0("Output file updated..."))
@@ -110,14 +116,23 @@ cat(file = "enriched_pathways.txt",
     "pathway_db\tTerm\tAdjusted.P.value\n",
     append = F)
 
-pathway_dbs <- config[config$type == "pathway","resource"]
+pathway_dbs <- config[config$type == "pathway_db","resource"]
 
 enriched_pathways <- enrichr(input, databases = pathway_dbs)
 
-adj_pathways <- lapply(enriched_pathways, function(x) x[x$Adjusted.P.value < 0.1, ])
+adj_pathways <- lapply(enriched_pathways, 
+                       function(x) {
+                          selected <- which(x$Adjusted.P.value < 0.1)
+                          ### Cap the amount of pathways to the predefined max in config
+                          cap <- min(length(selected), config[config$resource == "max_areas_per_pathway_db",]$value)
+                          selected <- head(selected, cap)
+                          x[selected, ]
+                        })
 
 for(aep in 1:length(adj_pathways)) {
-  write.table(cbind(pathway_db = pathway_dbs[aep], adj_pathways[[aep]][,c("Term","Adjusted.P.value")], stringsAsFactors = F), 
+  write.table(cbind(pathway_db = pathway_dbs[aep], 
+                    adj_pathways[[aep]][,c("Term","Adjusted.P.value")], 
+                    stringsAsFactors = F), 
               file = "enriched_pathways.txt", sep = "\t", quote = F, col.names = F, row.names = F, append = T)
 }